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By the time Camilla Black Grondahl became pregnant with her second child in 2010, she had already watched two older sisters bury sons who were born with a congenital affliction that gave them the appearance of “little old men.” Various health problems made their survival impossible.

The young mother did not know whether she, too, could pass the condition to her unborn son. But a Utah researcher, who had been sequencing her family’s genes, did know.

Gholson Lyon’s research team had detected a mutation in her genome that gave any boy she conceived a 50-50 chance of sharing the heartbreaking fate of his cousins and uncles.

“My jaw dropped open. Who would have thought that another mother would get pregnant during this research and it would be a boy?” said Lyon, then a professor of psychiatry leading the University of Utah’s genetic research into the disease.

He found himself in an ethical quandary that is bound to become more common in biomedical research. As technology advances and costs come down, gene sequencing is becoming routine — yet no system is...